Publications by Francesco Piazza

Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network

Paolo De Los Rios, Shiling Liang, Francesco Piazza, Daniel Maria Busiello

The exclusive presence of beta -D-ribofuranose in nucleic acids is still a conundrum in prebiotic chemistry, given that pyranose species are substantially more stable at equilibrium. However, a precise characterisation of the relative furanose/pyranose fra ...

Nature Research2021

Dissipation-driven selection of states in non-equilibrium chemical networks

Paolo De Los Rios, Shiling Liang, Francesco Piazza, Daniel Maria Busiello

Life has most likely originated as a consequence of processes taking place in non-equilibrium conditions (e.g. in the proximity of deep-sea thermal vents) selecting states of matter that would have been otherwise unfavorable at equilibrium. Here we present ...

2021

Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces

Paolo De Los Rios, Giuseppe Foffi, Francesco Piazza

In this paper we introduce a fully flexible coarse-grained model of immunoglobulin G (IgG) antibodies parametrized directly on cryo-EM data and simulate the binding dynamics of many IgGs to antigens adsorbed on a surface at increasing densities. Moreover, ...

Public Library Science2016

Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics

Matteo Dal Peraro, Enrico Spiga, Luciano Andres Abriata, Francesco Piazza

We present herein a thorough description of the effects of high glucose concentrations on the diffusion, hydration and internal dynamics of ubiquitin, as predicted from extensive molecular dynamics simulations on several systems described at fully atomisti ...

Amer Chemical Soc2014

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012) PREFACE

Giuseppe Foffi, Francesco Piazza

Iop Publishing Ltd2013

First-order coil-globule transition driven by vibrational entropy

Paolo De Los Rios, Francesco Piazza, Carlo Maffi

By shifting the balance between conformational entropy and internal energy, polymers modify their shape under external stimuli, such as changes in temperature. Prominent among such transformations is the coil-globule transition, whereby a polymer can switc ...

Nature Publishing Group2012

Inertial effects in diffusion-limited reactions

Nicolas Dorsaz, Giuseppe Foffi, Francesco Piazza

Diffusion-limited reactions are commonly found in biochemical processes such as enzyme catalysis, colloid and protein aggregation and binding between different macromolecules in cells. Usually, such reactions are modeled within the Smoluchowski framework b ...

Institute of Physics2010

Vibrational entropy and the structural organization of proteins

Paolo De Los Rios, Francesco Piazza

In this paper we analyze the vibrational spectra of a large ensemble of non-homologous protein structures by means of a novel tool, that we coin Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the intrinsic heterogeneity of force c ...

2010

On inconsistent entities. A reply to Colyvan

Francesco Piazza

In a recent article M. Colyvan has argued that Quinean forms of scientific realism are faced with an unexpected upshot. Realism concerning a given class of entities, along with this route to realism, can be vindicated by running an indispensability argumen ...

2010

Simple Monte Carlo model for crowd dynamics

Francesco Piazza

In this paper, we introduce a simple Monte Carlo method for simulating the dynamics of a crowd. Within our model a collection of hard-disk agents is subjected to a series of two-stage steps, implying (i) the displacement of one specific agent followed by ( ...

2010